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Welcome to Micro 22. Principles of Microbiology Tim K. Revell, Ph.D. What is Microbiology?. Root words: Micro = small Bio = life Logy = study of. Microorganisms (or Microbes). Organisms (living things) too small to be seen with the naked eye OR

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Welcome to micro 22

Welcome to Micro 22

Principles of Microbiology

Tim K. Revell, Ph.D.

What is microbiology

What is Microbiology?

Root words:

Micro = small

Bio = life

Logy = study of

Microorganisms or microbes

Microorganisms (or Microbes)

Organisms (living things) too small to be seen with the naked eye


Organisms too small to be seen without a microscope

Types of microbes

Types of Microbes

  • 1) Bacteria

Types of microbes1

Types of Microbes

  • 2) Archaea

  • Like bacteria, but different (more to come!)

  • Life’s extremes (Hydrothermal vents)

  • Not known to cause disease

Types of microbes2

Types of Microbes

  • 3) Protozoa

  • Mostly single-celled organisms with a nucleus

Types of microbes3

Types of Microbes

  • 4) Fungi (molds & yeast)

Types of microbes4

Types of Microbes

  • 4) Parastic worms

Welcome to micro 22

  • 5) Viruses

But are microbes good or bad

But are microbes good or bad?


Can cause illness

Can damage food crops


Good microbes can defend against bad microbes

Used in making yogurt, birth control pills, meat tenderizers

9 out of 10!

Field of microbiology

Field of Microbiology

  • A) Parasitology

  • B) Immunology

  • C) Bacteriology

  • D) Mycology

  • E) Virology

  • F) Our emphasis will be on Medical Microbiology

Some terms we use

Some terms we use…

  • Organisms: Any living thing

  • Microorganism: Any living thing that is generally microscopic in form

  • ___________: Disease Causing organism or agent.

  • Words in RED are GREAT options for “fill-in-the-blank” types of questions!

More terms

More Terms!....

  • __________: A state where the host (such as a human) harbors microbes that survive and multiply in or on body tissue.

  • __________: A process or event that results in any changes from the general state of good health.

  • __________________________: the damaging result of infection caused by microbes

  • _____________ disease causing ability OR the ability of a pathogen to gain entry to host tissues and bring about disease.

And yet even more terms

And yet, even more terms!

  • ____________: Degree of pathogenicity or the degree to which a pathogen causes a disease.

    Example: Salmonella

    Estimated 2-4 million cases/yr in U.S.

    Associated with raw meat, poultry, milk, dairy products, fish, eggs, coconut, frog legs, peanut butter, cocoa and chocolate, Pets! (such as turtles, other reptiles, dogs, cats, birds, pet food, treats)!

Changes in our understanding

Changes in our understanding….

  • _______________________ - clusters of genes (genetic information) responsible for virulence can move a pathogenic strain into avirulent organism converting it into a pathogen!



  • When two organisms live to together

Normal flora

Normal Flora

  • Locations of normal microbiota on and in the human body.

  • Over 1000 species in the mouth!

  • 99% of the cells on our body our not ours!

Normal microbiota and the host you

Normal Microbiota and the host (you!)

  • Microbial antagonism is a competition between microbes

  • Normal microbiotaprotect you by:

    • Occupying niches that pathogens might occupy

    • Producing acids

    • Producing _____________ (bacterial toxins that prevent the growth of other bacteria!)

  • ___________ – live microbes applied to or ingested into the body

  • ___________ – chemicals that promote bacterial growth.

Opportunistic microbes

Opportunistic Microbes

  • Normally do not cause disease…

  • But!...

    • Host becomes weakened

      • AIDS and Pneumocystispneumonia

    • Microbes in a different environment

      • E. coli in food…

    • Cooperation among microbes

      • ____________________a disease caused by more than one organism (often are synergistic – one alters the environment for the other!)

Classifying infectious diseases

Classifying Infectious Diseases

  • _______ a change in body function that is felt by a patient as a result of disease.

  • _______ a change in a body that can be measured or observed as a result of disease.

  • __________: A specific group of signs and symptoms that accompany a disease.

Occurrence of disease

Occurrence of Disease

  • ____________ The fraction of a population that contracts a disease during a specific time.

    • An indicator of the spread of a disease (RATE)

  • ____________ The fraction of a population having a specific disease at a given time.

    • Regardless of when it first appeared

    • Takes into account both old an new cases (SNAPSHOT).

      INCIDENCE is more of a RATE at which a disease is spreading….PREVALENCE is a measure of how widespread a disease is.

Occurrence of disease1

Occurrence of Disease

  • ____________ Diseases that occur occasionally in a population.

    • Most days, no cases (Plague or Rabies in humans)

  • ____________ Disease constantly present in a population.

    • Can be endemic from very low level (Syphillis) to nearly universal (herpes)



  • ___________ Disease acquired by many hosts (people) in a given area in a short period of time.

    • Disease could normally be either sporadic or endemic (Example, Hepatitis A at certain times).

      ______________ Worldwide epidemic

      _____________ – Immunity in most of a population (80%)

Severity or duration of a disease

Severity or Duration of a Disease

  • ____________ Symptoms develop rapidly.

  • ____________ Disease develops slowly.

    • These terms are NOT necessarily tied to how “bad” a disease is!

    • Latent Diseases – Diseases that appear to disappear and reappear (TB)

Extent of host involvement

Extent of Host Involvement

  • _____________ Pathogens are limited to a small area of the body.

  • ______________ An infection throughout the body.

  • _____________ Systemic infections that began as local infection

  • ____________ Bacteria in the blood

  • _____________ Growth of bacteria in the blood.

Extent of host involvement1

Extent of Host Involvement

  • ________________ Toxins in the blood

  • ________________ Viruses in the blood

  • ________________ Acute infection that causes the initial illness

  • ________________ Opportunistic infection after a primary (or predisposing) infection.

  • ______________ No noticeable signs or symptoms (inapparent infection).

Predisposing factors

Predisposing Factors

  • Make the body more susceptible to disease:

    • Short urethra in females (UTI’s)

    • Genetics

    • Climate and weather

    • Fatigue

    • Age

    • Lifestyle (stress!)

    • Chemotherapy

Course of disease

Course of disease

Course of disease1

Great Essay Question!

Course of Disease

  • 1)_____________ Pathogen enters host body, overcomes host defenses, and initiates parasitism.

  • 2) _____________ time between infection and appearance of first symptoms

    • Hours to years

    • Pathogen may be multiplying, adapting to new host, migrating through host body. This is OFTEN when pathogen is most contagious!

Course of disease2

Course of Disease

  • 3)_____________ Appearance of nonspecific symptoms (often fever, headache, malaise

    • Usually can not diagnose by prodromal symptoms

      • Contagious period: for many diseases, most contagious time is last half of incubation period and prodromal period.

Course of disease3

Course of Disease

  • 4)___________________ appearance of specific symptoms

    • May be specific enough to allow symptomatic diagnosis

    • Period of illness and period of decline

  • 5) _______________ Period of recovery from illness

    • Some pathogens remain alive in body

    • Possibility of relapse (return of symptoms)

Course of disease4

Course of disease

  • Level of recovery:

  • Recovery with immunity: will probably not have disease again (Chicken Pox)

  • Recovery without immunity: may have same disease again

  • Recovery as a carrier of pathogen

    • No symptoms, but shedding pathogen and able to infect other people

    • Carrier state may last from days to lifetime

    • May go directly from infection to carrier state!

Spread of infection

Spread of infection

  • Reservoirs of infection are continual sources of infection.

    • Human – HIV, Gonorrhea

      • Carriers may have in apparent infections or latent infections.

    • Animal – Rabies, Lyme Disease

    • Abiotic (nonliving)

      • Water – Cholera, Typhoid Fever.

      • Soil – Botulism, Tetanus

Transmission of pathogens

Transmission of Pathogens

  • Transmission is How a pathogen is carried to a new host.

  • 1) Direct Contact (with infected host)

    • Kissing, sex, petting an animal, animal bite (including human!)

Welcome to micro 22

  • 2) Indirect Contact: via ________ contaminated inanimate object

Welcome to micro 22

  • 3) Droplet infection: Saliva or respiratory discharges traveling through the air (for <1 meter)

Welcome to micro 22

  • 4) Vehicle: Transmission by an inanimate reservoir (food, water).

Welcome to micro 22

  • 5) Airborne

    • Pathogen carried by air for > 1 meter

      • Measles virus, fungus spores

Welcome to micro 22

  • 6) Vectors: Arthropods (fleas, ticks, mosquitoes)

    • Mechanical or Biological

Welcome to micro 22

  • 6a) Mechanical Vector Transmission

Welcome to micro 22

  • 6b) Biological vector transmission

    • Pathogen reproduces in vector


____________ infections

  • Infections acquired as a result of a hospital stay.

  • 5-15% of all hospital patients acquire nosocomial infections!







Welcome to micro 22

Nosocomial Infections

Common causes of nosocomial infections

Common Causes of Nosocomial Infections

Ways to prevent nosocomial infections

Ways to prevent Nosocomial infections…

Emerging infectious diseases

Emerging Infectious Diseases

  • Diseases that are new, increasing in incidence, or showing a potential to increase in the near future.

  • Contributing factors

    • Genetic recombination

      • E. coli 0157, Avian influenza (H5N1), Swine Flu (H1N1)

    • Evolution of new strains

      • V. cholerae 0139

    • Inapproriate use of antibiotics and pesticides

      • Antibiotic resistant strains

Welcome to micro 22


  • The study of where and when diseases occur and how they are transmitted in populations

Figure 14.10

Cdc centers for disease control and prevention atlanta ga

CDC (Centers for Disease Control and Prevention), Atlanta, GA

Centers for disease control and prevention cdc

Centers for Disease Control and Prevention (CDC)

  • ___________: Incidence of a specific notifiable disease.

  • Mortality: Deaths from notifiable diseases.

  • Morbidity rate: Number of people affected in relation to the total population in a given time period.

  • Mortality rate: Number of deaths from a disease in relation to the population in a given time.

Welcome to micro 22

Centers for Disease Control and Prevention (CDC)

  • Collects and analyzes epidemiological information in the United States.

  • Publishes Morbidity and Mortality Weekly Report (MMWR) www.cdc.gov

Microbial world defined by cell type

Microbial world defined by cell type

  • Cell= the fundamental unit of all life and carries out all basic functions of living things.

  • Two Types:

    • _____________ cells such as bacteria and archaea that have single circular chromosome, ribosomes, but no membrane bound organelles. Usually small.

    • _____________ cells such as fungi, worms, animals, plants that have chromosomes enclosed by a nuclear envelope, ribosomes and membrane bound organelles such as mitochondria. Usually larger.

Prokaryotic vs eukaryotic

Prokaryotic vs. Eukaryotic

Cell membrane cell wall capsule

cell membrane, cell wall, capsule

cell membrane


  • from intra- to extracellular (i.e. inside to outside cells)

cell wall



Procaryotic cells (bacteria) are relatively simple and

always unicellular.

Endosymbiotic theory

Endosymbiotic theory

  • eukaryotic cells came about when small prokcaryotic cells started living inside of larger prokaryotic cells

  • eukaryotic mitochondria and chloroplasts similar to bacteria: circular DNA, 70s ribosomes, fission, etc.

Procaryotic Eucaryotic Mitochondrion Chloroplast

Viruses and prions

Viruses and Prions

  • Viruses are non-living or semi-living

  • Prions are infection protein particles

  • All living things can:

    • Maintain Homeostasis

    • Reproduce

    • Require Energy

    • Have a genetic information base

    • Are capable of evolving.

Classifying organisms

Classifying Organisms

  • 1. The # and type of cells present.

    • Cell type is based on complexity, presence or absence of a cell wall.

Criterion 2 modes of nutrition

Criterion 2: Modes of nutrition

  • Nutrition refers to the means by which an organism obtains matter (e.g. for growth and repair) and energy (which drives life’s processes).

  • Sources of matter include 2 types:

  • organic: molecule containing both carbon and hydrogene.g. CH4, C6H12O6

  • inorganic: molecule not containing both C and H (could have one or the other or neither)e.g. NaCl, H2O, CO2

  • In addition, energy may be obtained from light or chemical sources.

Nutritional modes

Nutritional Modes

Another good essay question!

Carl linneaus

Carl Linneaus

  • Father of “_________”

  • Swedish botanist, physician, and zoologist

  • Wrote Systema Naturae in 1735

  • The science concerned with naming and classifying the diverse forms of life

Figure 10 1

3 Domain System!

Figure 10.1

The species concept

The Species Concept

  • 1. a group of individuals capable of mating and producing fertile offspring (or)

  • 2. a basic kind of organism

  • 3. Often has issues (particularly with bacteria!)



  • a group of closely related species; e.g.Clostridium tetaniClostridium botulinumClostridium perfringens

  • members of a genus will be the same in most respects; different in a few specific ways

  • placement in a genus is “a matter of opinion”

    • species are moved from genus to genus

    • Neisseria catarrhalis became Branhamella catarrhalis and is now Moraxella catarrhalis

    • Streptococcus lactis now Lactococcus (Streptococcus) lactis

    • Was based on shared properties vs. now evolutionary relationships

Some abbreviations

Some abbreviations

  • sp. Refers to species in singular. Often used to refer to an unknown species of a known genus, e.g. Mycobacterium sp.

  • spp. Refers to species in plural. Often used to refer to all members of a genus, e.g. Mycobacterium spp.

Subspecific levels of classification

Subspecific levels of classification

  • subspecies: group within a species, usually defined by visible traits; different subspecies usually live in different areas

  • strain: group within a species, usually defined by physiological traits

  • clone: group of organisms all derived from a single cell. All cells in the clone should be identical. However in some cases this isn’t so, and each such group is called a strain.

  • E.g. E. coli 0157:H7

  • E.g. Vibrio cholerae classic& Vibrio cholerae El Tor

  • Subspecies, strain, serotypemorpho type and variety areterms used



  • A group of individuals capable of reproducing (a species) that occupy the same place and time.

  • IMPORTANT for understanding evolution (genetic change in a group of organism over time).

Viruses are in a class by themselves

Viruses are in a class by themselves

  • Viruses are neither prokaryotic nor eukaryotic.

  • They are not considered “true cells” nor living by most scientists.

  • They are much simpler then even the simplest cells.

  • we consider them “microorganisms” due to their infectious nature.

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